Contacts of the helix formed by residues 157 - 171 (chain D) in PDB entry 2O1S
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ALA 157 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162C GLU* 4.8 0.7 - - - +
124D SER* 2.9 38.1 - - - +
154D ALA 3.4 1.0 + - - +
155D ILE 3.3 2.0 - - - -
156D THR* 1.3 78.9 + - - +
158D GLY* 1.3 67.2 + - - +
159D MSE 3.3 4.3 - - + +
160D ALA* 3.1 14.4 + - - +
161D PHE* 3.2 13.2 - - - -
368D ILE* 3.4 21.5 - - + +
398D ARG* 4.4 11.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 158 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C GLY* 3.3 35.1 - - - -
162C GLU* 3.0 21.8 + - - +
371C GLN* 4.9 0.6 - - - +
157D ALA* 1.3 73.0 - - - +
159D MSE 1.3 57.6 + - - +
161D PHE* 3.0 8.0 + - - +
162D GLU* 2.9 29.6 + - - +
371D GLN* 4.6 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 159 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371C GLN* 3.4 28.9 - - + +
372C HIS 4.7 2.2 - - - +
375C THR* 4.9 2.5 - - - -
402C GLN* 2.6 42.6 - - - +
406C ASP* 4.8 1.6 - - - +
124D SER* 3.3 36.1 - - - +
125D THR* 4.1 9.6 - - - -
128D SER* 3.9 11.6 + - - +
157D ALA* 4.5 1.3 - - + -
158D GLY* 1.3 76.3 - - - +
160D ALA* 1.3 58.3 + - - +
162D GLU* 3.8 12.9 - - - +
163D ALA* 2.9 31.0 + - - +
398D ARG* 2.9 39.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 160 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124D SER* 4.5 12.6 - - - +
127D ILE* 4.8 8.5 - - + -
150D ILE* 6.5 0.9 - - + -
154D ALA 4.0 14.6 - - - +
155D ILE* 3.9 27.4 - - + +
157D ALA 3.1 12.3 + - - +
159D MSE 1.3 82.9 - - - +
161D PHE* 1.3 58.4 + - - +
163D ALA* 3.5 5.5 + - - +
164D MSE 3.0 36.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 161 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161C PHE* 3.2 56.8 - + + -
162C GLU* 4.6 0.4 - - - -
165C ASN* 3.2 28.3 - - - -
246C LEU* 5.3 0.7 - - + -
155D ILE* 3.9 18.6 - - + -
156D THR* 3.7 23.1 - - - -
157D ALA 3.2 18.6 + - - -
158D GLY* 3.0 9.4 + - - +
160D ALA* 1.3 76.7 - - - +
162D GLU* 1.3 64.7 + - - +
164D MSE 4.0 8.2 - - - +
165D ASN* 3.0 31.8 + - - -
242D LEU* 3.7 27.8 - - + -
243D PHE* 6.1 0.4 - + - -
246D LEU* 4.6 12.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 162 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156C THR 4.3 7.0 - - - +
157C ALA* 3.8 5.9 - - - +
158C GLY* 2.9 28.8 + - - +
366C VAL 5.2 2.6 - - - +
368C ILE 4.1 0.3 - - - +
369C ALA* 3.1 37.6 - - + +
370C GLU 4.5 0.5 + - - -
371C GLN* 3.5 16.8 + - - +
372C HIS* 3.0 33.4 + - + +
398C ARG* 5.7 3.1 - - - -
158D GLY 2.9 18.5 + - - +
159D MSE 3.4 9.1 + - - +
161D PHE* 1.3 76.5 - - - +
163D ALA* 1.3 58.0 + - - +
165D ASN* 3.4 7.2 + - - +
166D HIS* 3.0 28.2 + - - +
371D GLN* 5.3 1.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 163 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372C HIS* 3.6 28.3 + - + +
127D ILE* 3.5 26.6 - - + +
128D SER* 3.7 9.4 - - - +
131D ILE* 4.6 2.0 - - + +
159D MSE 2.9 18.7 + - - +
160D ALA* 3.5 4.0 - - - +
161D PHE 3.1 0.2 - - - -
162D GLU* 1.3 73.8 - - - +
164D MSE 1.3 61.5 + - - +
166D HIS* 3.0 3.5 + - - +
167D ALA* 2.8 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 164 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127D ILE* 3.8 17.5 - - + -
155D ILE* 4.0 17.5 - - - -
160D ALA 3.0 23.2 + - - +
161D PHE* 3.4 6.7 + - - +
163D ALA* 1.3 75.7 - - - +
165D ASN* 1.3 56.7 + - - +
167D ALA* 4.2 0.2 - - - -
168D GLY 2.8 23.7 + - - -
243D PHE* 3.3 31.2 - - + -
246D LEU* 3.6 28.5 - - + +
248D PHE* 3.4 36.1 - - + -
277D PHE* 3.3 40.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 165 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156C THR* 5.0 4.5 + - - +
161C PHE* 2.8 41.0 - - - -
161D PHE 3.0 20.6 + - - +
162D GLU* 3.5 7.1 - - - +
164D MSE 1.3 75.5 - - - +
166D HIS* 1.3 65.0 + - - +
168D GLY* 3.2 2.3 + - - -
169D ASP* 3.0 22.5 + - - +
246D LEU* 3.7 23.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 166 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364C PHE* 4.3 8.8 - + - +
365C ASP 4.3 18.0 + - - -
366C VAL* 3.6 26.9 - - + +
372C HIS* 2.8 35.5 - + + +
376C PHE* 3.9 15.5 - + - -
131D ILE* 3.0 20.4 - - + +
162D GLU 3.0 10.5 + - - +
163D ALA 3.0 4.7 + - - +
165D ASN* 1.3 76.6 - - - +
167D ALA* 1.3 63.6 + - - +
169D ASP* 3.0 9.2 + - + +
170D ILE* 2.9 54.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 167 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127D ILE* 5.4 0.4 - - + -
131D ILE* 4.3 18.8 - - + +
163D ALA 2.8 16.1 + - - +
164D MSE 3.6 4.9 - - - +
166D HIS* 1.3 77.7 - - - +
168D GLY* 1.3 56.0 + - - +
170D ILE* 4.3 1.8 - - - -
171D ARG* 2.7 35.7 + - - -
172D PRO* 3.3 16.6 - - + +
174D MSE 4.5 4.7 - - - -
248D PHE* 3.6 22.2 - - + -
275D PRO* 3.6 5.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 168 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164D MSE 2.8 12.5 + - - -
165D ASN 3.2 1.8 + - - -
167D ALA* 1.3 76.9 - - - +
169D ASP* 1.3 58.9 + - - +
171D ARG* 3.4 17.5 - - - -
246D LEU 3.4 23.3 - - - -
247D GLY* 4.1 16.2 - - - -
248D PHE* 4.4 1.3 - - - -
275D PRO* 4.7 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 169 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365C ASP 4.7 6.1 - - - +
165D ASN 3.0 12.9 + - - +
166D HIS* 3.0 16.6 + - + +
168D GLY* 1.3 80.5 - - - +
170D ILE* 1.3 74.9 + - - +
171D ARG* 3.8 6.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 170 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364C PHE* 4.7 14.4 - - + -
131D ILE* 3.7 17.5 - - + -
135D VAL* 3.8 15.0 - - + -
166D HIS* 2.9 49.6 + - + +
169D ASP* 1.3 85.5 - - - +
171D ARG* 1.3 70.9 + - - +
172D PRO* 3.5 26.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 171 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167D ALA 2.7 18.9 + - - -
168D GLY 3.4 17.0 + - - +
169D ASP 3.8 11.0 - - - +
170D ILE* 1.3 78.3 - - - +
172D PRO* 1.3 68.5 - - - +
173D ASP* 3.9 2.8 + - - +
247D GLY* 3.3 24.7 + - - -
273D LYS 4.8 3.8 + - - -
274D GLY* 4.1 18.6 - - - -
275D PRO* 3.7 21.2 + - + +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il